Re: [ccp4bb] TLS, NCS and refinement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: activation of thiol group
From: Deepak Oswal deeposwal {- at -} GMAIL {- dot -} COM
Date: 2010-03-29

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Subject: Re: activation of thiol group
From: "Soisson, Stephen M" stephen_soisson {- at -} MERCK {- dot -} COM
Date: 2010-03-29

Subject: Re: TLS, NCS and refinement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-03-29

Just some ideas. NCS usually good with 2.7A data, TLS only to be used
when model is complete..

You say Matthews suggest 11 molecules, but you only find 6 - doesnt
this mean you have a very high solvent content?

I would check the MR carefully.
How are the 6 molecules related - are there dimer, trimers? etc.
I submit the coordinates to PISA to get a good answer about this, and to
return the most compact packed structure.

And does the self rotation agree with the above findings?

If so rebuild and refine a bit till R factors stop reducing, then redo
the MR with the larger unit.. USE NCS at all times - cetainly till the
Rfactors have fallen below 30%

Then once you think you have the complete and more or less corrected
structure introduce TLS choosing the features to restrain together
carefully. Maybe each complex belongs as a unit, or maybe a larger complex..

Eleanor

Daniel Bonsor wrote:
> Hello again...
>
> I have a 2.7A resolution data set. Spacegroup P212121 as suggested by Pointless and best space group when run through Phaser. Unit cell is 110.02x160.49x186.55. Mathew's suggest 11 complexes in ASU. Both Molrep and Phaser can only find 6. This seems to be a typical observation with the complexes that we solve (high solvent content).
>
> Due to the low(ish) resolution I wish to apply TLS and NCS during refinement. My question(s) is when to apply TLS and NCS, the order in which it should be done, and when to switch off NCS (if at all) during the stages of refinement. I have used a homologue complex (Protein A -100% identical, Protein B - 80% identical) as a model.
>
> I am open to any and all suggestions on the matter.
>
>
> Thanks in advance
>
> Dan

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: activation of thiol group
From: Deepak Oswal deeposwal {- at -} GMAIL {- dot -} COM
Date: 2010-03-29

Next message:
Subject: Re: activation of thiol group
From: "Soisson, Stephen M" stephen_soisson {- at -} MERCK {- dot -} COM
Date: 2010-03-29